Hello,
On Oct 16, 2010, at 12:40 AM, ying yu <helen.yingyu.gmail.com> wrote:
> When I compile the mpi CPU version,
>
> In the $AMBERHOME/AmberTools/src
>
> ./configure –mpi gnu
>
> Make parallel
>
> The mpi version pmemd could be built successfully.
>
>
>
> But If I use:
>
> ./configure –mpi intel
>
> There is no error in this step,
>
> When I do : make parallel
>
> There will comes out:
There are a lot of things that can go wrong here. First, does Amber compile ok in serial with the intel compilers? If not, it's likely that your environment is not set up correctly. If it does, then you can move on to the parallel compilation. However, the parallel build assumes several things. First, it assumes that you have a working MPI implementation that conforms to the MPI standard, such as openMPI, MPICH2, etc. Finally, and this is where I think you are getting hit, it assumes that mpif90 and mpicc invoke the compilers you specified on the command line. You can check which compilers are used by the mpi wrappers by typing "mpif90 -show" and "mpicc -show" into the terminal. If you see that it is invoking gfortran and/or gcc, then you have a problem. Typically, you need to maintain two separate MPI implementations to use two different compilers for parallel amber. You also have to take care to keep them separate so they don't clobber one another.
You do, of course, have to do a make clean like Bill said before starting a new compilation, or it will attempt to use old object files created by the old compilers.
Hope this helps,
Jason
>
>
>
> gcc: language Host not recognized
>
> gcc: language Host not recognized
>
> gcc: rand2.c: linker input file unused because linking not done
>
> mpicc -c -Dflex -ip -O3 -xHost -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -DBINTRAJ -DMPI -o sasad.o sasad.c
>
> gcc: language Host not recognized
>
> gcc: language Host not recognized
>
> gcc: sasad.c: linker input file unused because linking not done
>
> flex -t mm_options.l | sed -e 's/{stdout}/{DONTchangeSTDOUThere}/' -e
> 's/yy/mmo/g' -e 's/stdout/nabout/' -e 's/DONTchangeSTDOUThere/stdout/' >
> lex.mm_options.c
>
> mpicc -c -Dflex -ip -O3 -xHost -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -DBINTRAJ -DMPI -o sff.o sff.c
>
> gcc: language Host not recognized
>
> gcc: language Host not recognized
>
> gcc: sff.c: linker input file unused because linking not done
>
> mpicc -c -Dflex -ip -O3 -xHost -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -DBINTRAJ -DMPI -o time.o time.c
>
> gcc: language Host not recognized
>
> gcc: language Host not recognized
>
> gcc: time.c: linker input file unused because linking not done
>
> mpicc -c -Dflex -ip -O3 -xHost -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -DBINTRAJ -DMPI -o traceback.o traceback.c
>
> gcc: language Host not recognized
>
> gcc: language Host not recognized
>
> gcc: traceback.c: linker input file unused because linking not done
>
> mpicc -c -Dflex -ip -O3 -xHost -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -DBINTRAJ -DMPI -o xminC.o xminC.c
>
> gcc: language Host not recognized
>
> gcc: language Host not recognized
>
> gcc: xminC.c: linker input file unused because linking not done
>
> rm -f libsff.a
>
> ar rv libsff.a binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o
> nmode.o prm.o rand2.o sasad.o sff.o time.o traceback.o xminC.o
>
> ar: creating libsff.a
>
> ar: binpos.o: No such file or directory
>
> make[2]: *** [libsff.a] Error 1
>
> make[2]: Leaving directory
> `/home/yiyu/Amber-withlicense/amber/AmberTools/src/sff'
>
> make[1]: *** [libsff] Error 2
>
> make[1]: Leaving directory
> `/home/yiyu/Amber-withlicense/amber/AmberTools/src/nab'
>
> make: *** [parallel] Error 2
>
>
>
> seems it doesn’t use icc as the compiler, did I miss something?
>
>
>
> Thanks,
>
>
>
> Ying
>
> --
> Happy Helen
>
>
>
> --
> Happy Helen
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Oct 16 2010 - 07:00:04 PDT
